[khmer] normalize-by-median.py - IOError: [Errno 30] Read-only file system:

C. Titus Brown ctb at msu.edu
Thu Jul 3 07:42:31 PDT 2014


OK, very weird :).  Are you using virtualbox, by any chance?

https://github.com/pypa/virtualenv/issues/209

cheers,
--titus

On Wed, Jul 02, 2014 at 04:36:02PM -0500, Efraim Rodrigues wrote:
> Hi, Titus.
> 
> Yes, I have the privileges to write. The instruction 'touch' worked, but I
> still have the error.
> 
> Regards,
> 
> 
> On Wed, Jul 2, 2014 at 12:53 PM, C. Titus Brown <ctb at msu.edu> wrote:
> 
> > Hi Efraim,
> >
> > looks to me like the directory you're running normalize-by-median.py in
> > is mounted read-only -- could be incompatibility, could be just mounted
> > that way.  Try doing 'touch jjj' to see if you have write privileges;
> > if that works then something strange is going on :).
> >
> > One likely confusion here is that most of our scripts write output files
> > into
> > the current working directory.  That's intentional design but not
> > particularly standard...
> >
> > Let us know how it goes!
> >
> > cheers,
> > --titus
> >
> > On Wed, Jul 02, 2014 at 11:41:00AM -0500, Efraim Rodrigues wrote:
> > > Greetings Ramakrishnan,
> > >
> > > Thank you for quick reply.
> > >
> > > This is the output for 'uname -a', 2.6.32-431.11.2.el6.x86_64 #1 SMP Tue
> > > Mar 25 11:15:18 CDT 2014 x86_64 x86_64 x86_64 GNU/Linux
> > >
> > > My output for 'mount' is "type nfs
> > > (rw,nfsvers=3,rsize=32678,wsize=32678,noacl,sloppy)".
> > >
> > > Thank you!
> > >
> > >
> > > On Wed, Jul 2, 2014 at 11:28 AM, Ramakrishnan Srinivasan <ramrs at nyu.edu>
> > > wrote:
> > >
> > > > Hello Efraim,
> > > >
> > > > Thank you for using khmer. This looks like an error owing to
> > incompatible
> > > > file system formats.
> > > >
> > > > This might happen if we tried writing to an incompatible file system
> > (say,
> > > > NTFS) from certain versions of Linux. Any information on the exact
> > Linux
> > > > distro+version you're running and the filesystem format of the
> > partition
> > > > you are writing to would help.
> > > >
> > > > Could you maybe give us the output of the following commands:
> > > > `uname -a`
> > > > `mount`
> > > >
> > > > Thank you!
> > > >
> > > >
> > > >
> > > > --
> > > > Ram
> > > >
> > > >
> > > > On Wed, Jul 2, 2014 at 12:13 PM, Efraim Rodrigues <
> > efraimnaassom at gmail.com
> > > > > wrote:
> > > >
> > > >> Greetings,
> > > >>
> > > >> Before running normalize-by-median.py, I ran interleave-reads.py which
> > > >> generated a 'se' file. Then, it looks like the normalize-by-median.py
> > > >> requires special rights to work on this output file from
> > > >> interleave-reads.py and even though I have already set all possible
> > rights,
> > > >> it is still returning the error  IOError: [Errno 30] Read-only file
> > system:
> > > >>
> > > >> I looked it up on github issues and khmer.readthedocs.org/ but I
> > could
> > > >> not find anything related to it. Thus, has anyone faced this problem
> > before?
> > > >>
> > > >> Regards,
> > > >> Efraim Rodrigues.
> > > >>
> > > >> _______________________________________________
> > > >> khmer mailing list
> > > >> khmer at lists.idyll.org
> > > >> http://lists.idyll.org/listinfo/khmer
> > > >>
> > > >>
> > > >
> >
> > > _______________________________________________
> > > khmer mailing list
> > > khmer at lists.idyll.org
> > > http://lists.idyll.org/listinfo/khmer
> >
> >
> > --
> > C. Titus Brown, ctb at msu.edu
> >

-- 
C. Titus Brown, ctb at msu.edu



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